Merge branch 'release/v.0.9.8' into develop

ChangeLog.md

@@ -1,9 +1,35 @@
+# Ver. 0.9.8 (2016-7-14)
+
+## New
+
+- New tag ``HESSIAN`` in program **alm** for printing entire Hessian matrix
+- New tag ``KAPPA_SPEC`` in **anphon** for calculating spectra of thermal conductivity
+- New option ``--offset`` in **extract.py** for subtracting residual forces (displacements) in an equilibrium structure from training data sets. We recommended to use this option if internal coordinates of atoms (Wyckoff potisions) have free parameters.
+- New option ``--isotope`` in **analyze_phonons.py**
+
+## Changes
+
+- Improve the performance of thermal conductivity calculations with the tetrahedron method (``ISMEAR=-1``). The new version is <Font color='red'>more than 3 times faster</font> than the previous version.
+- Improve the efficiency of the algorithm for generating constraings for the translational invariance
+- Avoid 'NaN' in thermal conductivity calculations with imaginary branches
+- Loosen the default value of ``TOLERANCE`` for detecting crystal symmetry
+- Stop printing the CLASSICAL entry in PREFIX.result files
+- Change the unit of the smearing width written in PREFIX.result files (a.u. --> cm^-1)
+
+## Fix
+
+- Fixed an issue regarding the phonon-isotope scattering rate
+- Fixed a bug in relaxation.cpp regarding the permutation symmetry of q mesh
+- Fixed an invalid memory reference in **analyze_phonons.cpp**
+- Added a routine to check the consistency of the crystal structure when the ``FC2XML`` tag is used in **anphon**
+
+
 # Ver. 0.9.7 (2016-3-10)
 
 ## New
 
-- New option SPS = 2 for anphon
-- New tag MAGMOM for considering collinear spin (alm). The format is same as VASP.
+- New option ``SPS = 2`` in anphon
+- New tag ``MAGMOM`` for considering collinear spin (alm). The format is same as VASP.
 - ALAMODE logo 
 
 ## Changes
@@ -25,24 +51,24 @@
 - anphon code incorrectly printed RMSD instead of MSD in previous versions. Fixed.
 - qe2alm.cpp now works with ibrav=0.
 - Fixed several issues in displace.py and extract.py for processing QE files.
-- PRINTPR now works properly when KPMODE = 0.
+- ``PRINTPR`` now works properly when KPMODE = 0.
 
 
 # Ver. 0.9.6 (2015-09-14)
 
 ## New
 
-- New option ICONST=11 for ALM which considers translational invariance algebraically
+- New option ``ICONST=11`` in **alm** which considers translational invariance algebraically
 
-- FC2XML-tag for ANPHON. Using this tag, it is now possible to employ different size of 
+- ``FC2XML``-tag in **anphon**. Using this tag, it is now possible to employ different size of 
    supercells for harmonic and anharmonic terms.
 
 - qe2alm.cpp in the tools/ directory which converts Quantum-ESPRESSO fc files to ALAMODE xml files.
 
 ## Changes
 
-- Changed the meaning of --calc=cumulative in analyze_phonons.py. 
-   The --calc=cumulative in the previous version is now equivalent to --calc=cumulative2.
+- Changed the meaning of ``--calc=cumulative`` in analyze_phonons.py. 
+   The ``--calc=cumulative`` in the previous version is now equivalent to ``--calc=cumulative2``.
 
 - Updated tutorial
 
@@ -79,7 +105,7 @@
 
 - New tag PRINTPR (anphon) for calculating (atomic) participation ratio
 
-- Implement ISOTOPE = 2 to print the selfenergy due to phonon-isotope scatterings (anphon)
+- Implement ``ISOTOPE = 2`` to print the selfenergy due to phonon-isotope scatterings (anphon)
 
 ## Changes
 
@@ -96,11 +122,11 @@
 
 ## New
 
-- New tag FC3XML (alm)
+- New tag ``FC3XML`` (alm)
 
-- New tag SPS (anphon) for calculating the scattering phase space  
+- New tag ``SPS`` (anphon) for calculating the scattering phase space  
 
-- New mode calc=kappa_boundary in analyze_phonons.py
+- New mode ``--calc=kappa_boundary`` in analyze_phonons.py
 
 ## Changes
 
@@ -130,7 +156,7 @@
 
 - Different algorithm for anharmonic scattering rates (a little performance improvement is expected)
 
-- PRINTVEL = 1 now print the xyz component
+- ``PRINTVEL = 1`` now print the xyz component
 
 - Renamed phonon_thermodynamics.{cpp,h} as thermodynamics.{cpp,h}
 
@@ -150,7 +176,7 @@
 
 - Python auxiliary tool for xTAPP
 
-- alm now checks if DFILE and FFILE have enough lines
+- alm now checks if ``DFILE`` and ``FFILE`` have enough lines
 
 ## Changes
 

LICENSE.txt

@@ -1,6 +1,6 @@
 The MIT License (MIT)
 
-Copyright (c) 2014 Terumasa Tadano
+Copyright (c) 2014,2015,2016 Terumasa Tadano
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
@@ -18,4 +18,4 @@ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+SOFTWARE.

README.md

@@ -1,5 +1,5 @@
 # ALAMODE 
-### Version 0.9.7 (Beta)
+### Version 0.9.8 (Beta)
 ![alt ALAMODE](./docs/img/alamode.png)
 
 - - -

docs/source/conf.py

@@ -62,7 +62,7 @@
 # The short X.Y version.
 version = '0.9'
 # The full version, including alpha/beta/rc tags.
-release = '0.9.7'
+release = '0.9.8'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

include/version.h

@@ -12,4 +12,4 @@
 
 #include <string>
 
-static const std::string ALAMODE_VERSION = "0.9.7";
+static const std::string ALAMODE_VERSION = "0.9.8";